SMTL ID : 5v3c.1

Crystal structure of TGT in complex with 4-(aminomethane)cyclohexane-1-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.309, C.311, V.313, C.314, H.340 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.309, A:C.311, A:C.314, A:H.340 ZN.8: 5 residues within 4Å: Chain B: C.309, C.311, V.313, C.314, H.340 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.309, B:C.311, B:C.314, B:H.340

2 x AMH: TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID(Non-covalent)

AMH.2: 12 residues within 4Å: Chain A: Y.97, D.147, C.149, I.192, Q.194, G.220, G.221, L.222, A.223, V.224, M.251, G.252 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.97, A:Y.97, A:Y.97, A:V.224, A:M.251 Hydrogen bonds: A:Q.194, A:G.221, A:L.222 AMH.9: 12 residues within 4Å: Chain B: Y.97, D.147, C.149, I.192, Q.194, G.220, G.221, L.222, A.223, V.224, M.251, G.252 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.97, B:Y.97, B:Y.97, B:V.224, B:M.251 Hydrogen bonds: B:Q.194, B:G.221, B:L.222

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: W.287, E.308, K.351, F.364, F.368, R.371 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.287, A:R.371, A:R.371 PEG.4: 9 residues within 4Å: Chain A: K.24, R.25, H.136, G.139, S.140, D.141, Q.183, N.186, A.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.136, A:D.141 Water bridges: A:Q.183, A:N.186 PEG.10: 6 residues within 4Å: Chain B: W.287, E.308, K.351, F.364, F.368, R.371 3 PLIP interactions: 3 interactions with chain B Water bridges: B:W.287, B:R.371, B:R.371 PEG.11: 9 residues within 4Å: Chain B: K.24, R.25, H.136, G.139, S.140, D.141, Q.183, N.186, A.187 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.136 Water bridges: B:Q.183, B:N.186

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 4 residues within 4Å: Chain A: F.7, S.8, I.9, D.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.9 DMS.6: 7 residues within 4Å: Chain A: P.47, E.48, R.51, G.85, W.86, D.87, R.88 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.87 DMS.12: 4 residues within 4Å: Chain B: F.7, S.8, I.9, D.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.9 DMS.13: 7 residues within 4Å: Chain B: P.47, E.48, R.51, G.85, W.86, D.87, R.88 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.87

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 6 residues within 4Å: Chain A: L.302, P.304, C.314, Q.315, W.317, S.318 No protein-ligand interaction detected (PLIP) PGE.14: 6 residues within 4Å: Chain B: L.302, P.304, C.314, Q.315, W.317, S.318 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hassaan, E. et al., Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies. Chemmedchem (2020)

Release Date

2018-05-16

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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